You'll need to convert the video to FLV which you can do when you import the video. AVI always seems to convert well. To jump to different parts of the video you need to learn about cue points http://www.communitymx.com/content/article.cfm?cid=124DB
It looks like you're asking for an unusual aspect ratio. Most video is wider that tall. You'll have to take that up with the videographer.
Is the videographer also the editor? If you're taking delivery of an edited video, then all you need to do is convert as stated above. The aspect ratio depends on how the video is shot, either 4:3 or 16:9. This can be changed in the editor if absolutely necessary, but some cropping will occur.
If I haven't done the editing and just need to prep the vid for web, I still want to have the highest quality least compressed format I can get. Sometimes AVI files are too big if I'm retrieving them via a download, so the next best thing is Quicktime. Don't let them burn it to a playable DVD, as then it's compressed to MPEG2 and doesn't translate well to FLV in my experience. You can use FLV, F4V or even mp4 files in but Flash player 9 or higher is required for playback.